I snapped last night and bought 3 bdm certificates, Johanna's death certificate, Dietrich's death certificate and Frederick Alfred's birth certificate (Frederick is my great grandfather and Johanna's last child).
Frederick Alfred's birth is the most interesting one. Its from 1893, and lists him as "Frederick Alfred Stendt"... not Davison, like the indexes say. His father is 'Illegitimate' and his mother is Johanna Davison, already living in Emily St Footscray (rather than Warrnambool). This pretty strongly suggests that Dietrich is the father, not Thomas.
Johanna's death certificate suggests she got married at age 30 in Melbourne (1889, not 1909 when it actually happened). I'm betting that's about the time she met/got together with Dietrich.
Dietrich's death certificate says he had been in Victoria since roughly 1885, and he got married in Fitzroy around 1886 to Johanna Matthew, with one issue, Frederick Alfred. At least this gives me a rough idea that only one of Johanna's children is Dietrich's too, but it does explain why the other children changed their names. (Have to take his info with a grain of salt, as he died much later than Johanna of senile dementia, so...)
Still no idea when/why Johanna and Thomas seperated, and I can't think of any other way to find out - although I'm tempted to post a letter to all the Stendt's in the whitepages and see if any of them are descendants too.
And to cap it off, one of my dad's cousins sent me this:
Grandpa, or was it Mum, told us the story of the two Stendt boys being on a ship that came to Melbourne. They "jumped ship" and ran most of the night to escape. Exhausted, they stopped against a large stone wall and slept until daylight. On waking, they looked up to see guards with guns pacing the wall above them - they had slept against the wall of Coburg Gaol!
... which might explain why Dietrich never shows up on the electoral roll - I figured he'd shown up after Federation and hadn't naturalised, but if he'd been in Melbourne since 1885 that seems less likely...